The Golden Gate Bridge has switched to "All Electronic" toll collection. 

There will only be a toll charge if you are traveleing southbound across the bridge. Northbound is free.

Unless you pay for the toll before you cross, your rental car company can charge fees and penalities.  Doing it as part of the rental car agreement will reduce the amounts of the additional costs, which will be automatically added to your credit/debit card as an additional amount.

The official Golden Gate Bridge website has a detailed list of the fees and rules for each participating Vehicle Rental Company.

If you are traveling in the area, be prepared.